It seems like the notification bar on the bottom of the desktop in Linux Mint 12 never hides unless I click N+1 times on it first (N being the number of messages). Since it's overlaid over all windows (even fullscreen video) it's a bit annoying. Right- and left-clicking the notification bar does not bring up any settings dialog, so I'm wondering how to either automatically hide messages after a timeout, disable the display of certain messages (I don't need to know about external disks which are plugged in at boot time), or (if all else fails) disable the notification bar altogether.
On Arch Linux I removed exec permission on notification-daemon lib. I found this temporary quick fix when I was searching for solution to this same problem.
$ sudo chmod -x /usr/lib/notification-daemon-1.0/notification-daemon
Some of annoying notifications you can disable here:
For example you can disable "Print Queue applet" and you wont get notification about every printed document. Or "Disk Notifications" and this should resolve your "Your USB disk is plugged in" notification problem.
I've decided to turn them completely off: in advanced settings, shell extensions, disable notifications extension